dbSNP rs1150064: EFCAB14:c.1312+928A>T (chr1-46682372-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014774.3(EFCAB14):c.1312+928A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,976 control chromosomes in the GnomAD database, including 13,916 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13916 hom., cov: 32)

Exomes 𝑓: 0.21 ( 0 hom. )

Consequence

EFCAB14
NM_014774.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

Publications

3 publications found

Variant links:

Genes affected

EFCAB14 (HGNC:29051): (EF-hand calcium binding domain 14) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

EFCAB14 links:

EFCAB14-AS1 (HGNC:44108): (EFCAB14 antisense RNA 1)

EFCAB14-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014774.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EFCAB14	NM_014774.3	MANE Select	c.1312+928A>T	intron	N/A	NP_055589.1	O75071
EFCAB14-AS1	NR_038827.1		n.268+108T>A	intron	N/A
EFCAB14-AS1	NR_038828.1		n.185-4301T>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EFCAB14	ENST00000371933.8	TSL:1 MANE Select	c.1312+928A>T	intron	N/A	ENSP00000361001.3	O75071
EFCAB14	ENST00000674415.1		c.*872A>T	3_prime_UTR	Exon 10 of 10	ENSP00000501464.1	A0A6I8PU78
EFCAB14	ENST00000672422.2		c.1405+928A>T	intron	N/A	ENSP00000499873.2	A0A804H3B5

Frequencies

GnomAD3 genomes

AF:

0.400

AC:

60664

AN:

151824

Hom.:

13858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.581

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.406

GnomAD4 exome

AF:

0.206

AC:

AN:

Hom.:

AF XY:

0.231

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.561

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.400

AC:

60785

AN:

151942

Hom.:

13916

Cov.:

AF XY:

0.407

AC XY:

30229

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.581

AC:

24072

AN:

41422

American (AMR)

AF:

0.453

AC:

6918

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1266

AN:

3468

East Asian (EAS)

AF:

0.779

AC:

4016

AN:

5158

South Asian (SAS)

AF:

0.408

AC:

1964

AN:

4810

European-Finnish (FIN)

AF:

0.294

AC:

3097

AN:

10550

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18256

AN:

67936

Other (OTH)

AF:

0.413

AC:

872

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1711

3422

5134

6845

8556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.335

Hom.:

1175

Bravo

AF:

0.420

Asia WGS

AF:

0.604

AC:

2099

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.0

(source)

DANN

Benign

0.81

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over